The team began play in the 1958 season as an independent school in the NCAA College Division, made up of the athletic programs of small universities and colleges. The school, founded in the early 1950s, was then known as the San Diego College for Men, and its athletic programs were known as the Pioneers. Mike Morrow was the program's head coach for its first six seasons (1958-1963), and the team had an 82-64 record during his tenure. In 1961, the school's athletic programs were renamed the Toreros, for the Roman Catholic school's connections to Spain.
In 1964, John Cunningham became the program's second head coach. In 1966, the team joined its first conference, the College Division's Southern California Athletic Conference (SCAC). In four seasons in the conference (1966-1969), the team had a conference record of 25-26-1. Prior to the 1970 season, the Toreros left the SCAC to become a College Division Independent again. Also in 1970, the team began playing in a new venue, which would eventually be dedicated to John Cunningham.
In 1972, the San Diego College for Men merged with the San Diego College for Women to form the University of San Diego.
Through the 1973 season, NCAA institutions had competed in two divisions– the large-school University Division and the small-school College Division. After the 1973 season, however, the NCAA reorganized into its modern, three-division format. The University Division became the modern Division I, while the College Division became Division II and Division III. San Diego, which had previously competed as a College Division Independent, became a Division II Independent.
The SCBA and NCBA stopped operating after the 1984 season, and the PCAC and WCAC returned to sponsoring separate baseball conferences. As a result, San Diego joined the WCAC following the 1985 season. Shortly thereafter (following the 1988 season), the conference was renamed the West Coast Conference (WCC). San Diego struggled in its first several seasons in the league, finishing no higher than fourth from 1985-1991. In 1992 and 1993, however, the Toreros had consecutive second-place finishes and consistently finished highly in the 1990s.
Following the 1998 season, John Cunningham retired after 35 seasons. The team's venue had been renamed John Cunningham Stadium in 1988, and Cunningham retired as San Diego's all-time wins leader with 843 wins. Then-San Francisco head coach Rich Hill was hired to replace Cunningham.
In 1999, Rich Hill's first season, the WCC split into two, four-team divisions, the West Division and the Coast Division. The Toreros finished third, second, and second in 1999, 2000, and 2001, respectively. The team then won the West Division and the West Coast Conference Championship Series in both 2002 and 2003, appearing in its first two NCAA Tournaments. San Diego again qualified for the tournament in 2006.
John Cunningham Stadium, located on the university's campus, was the program's home venue from prior to the 1970 season until after the 2012 season. Before the field's 1970 construction, the program had played at several different venues in San Diego. The field had a capacity of 1,200 spectators and was named for former San Diego head coach, John Cunningham, who coached the team from 1964-1998.
Beginning in the 2013 season, the team will play at Fowler Park, built on the location of Cunningham Stadium, which was demolished in summer 2012. Fowler has a capacity of 1,700 spectators that can be expanded to 3,000. The park is named for Ron and Alexis Fowler, who donated much of the stadium's $13 million construction cost. The playing field itself is named Cunningham Field, dedicated to the same coach for whom the program's former venue was named.
The team's most successful head coach is former coach John Cunningham, who won 843 games from 1964-1998. Also, Cunningham's 35 seasons as head coach make him the longest tenured coach in program history.
National champion Conference regular season champion Conference regular season and conference tournament champion Division regular season champion Division regular season and conference tournament champion Conference tournament champion
^Rider, Nate (July 31, 2012). "Muckdogs Down Staten Island in 11 Innings". TheDailyNewsOnline.com. Archived from the original on August 16, 2012. Retrieved August 16, 2012. "After looking over-matched in the ninth against James Pazos and on the first two pitches he saw from Varnadore, Montero fouled a pitch straight back and then proceeded to lace one directly over second base to plate the game-winner."